Interaction of Nickel(II) with histones: in vitro binding of nickel(II) to the core histone tetramer

Determination of the role of specific amino acids in the binding of Zn(II), Ni(II), and Cu(II) to the active site of the M10 family metallopeptidase

Metallopeptidases are a group of metal-dependent enzymes that hydrolyze peptide bonds. These enzymes found in Streptococcus pneumoniae assist the pathogen in infecting the host by breaking down host tissues and extracellular matrix proteins. Considering metallopeptidases' significant role in bacterial virulence, inhibiting this enzyme represents a promising avenue for research. These enzymes are characterized by the presence of Zn(II) in the active site, proper coordination of which is essential for their catalytic function. This work aims to determine the significance of the specific amino acids in the metal binding domain of metallopeptidase from S. pneumoniae. For this purpose, we investigated the coordination chemistry of Zn(II), Ni(II), and Cu(II) ions with point-mutated peptide models of the metal-binding domain. Mutations were introduced at His-2 (L1) and Glu-1. Studies have shown that at pH 7.14 (pH of infected lungs by S. pneumoniae), point mutation on glutamic acid caused only minor effects on the binding of Zn(II) and Ni(II), while significantly improving Cu(II) binding. The stability of copper complexes is greater with the mutant Glu-1 → Gln-1 than with the original domain due to a hydrogen bonding network created by the Gln backbone with its side chain. Substituting histidine resulted in a significant reduction in metal binding for all metal ions, highlighting the crucial role of His-2 in metal coordination. Introduced mutations at neutral pH did not significantly affect the secondary structure of metal complexes. However, at alkaline pH, the peptides showed a higher percentage of antiparallel β-sheet structures upon the addition of Cu(II), Ni(II) and Zn(II).

Exploring binding preferences: Cu(II), Ni(II), and Zn(II) complexes of mycobacterial GroEL1 His-rich and Glu/His-rich domains

Mycobacterial histidine-rich GroEL1 protein significantly differs from the well-known methionine-glycine-rich GroEL chaperonin and most preferably participates in Cu(II) homeostasis. Some GroEL1 proteins, however, do not possess six but only three histidine residues and more acidic residues that can function as binding sites for metal ions. To evaluate the importance of this difference, we examined and compared the properties of GroEL1 His-rich or Glu/His-rich C-terminal domains as ligands for Cu(II), Ni(II), and Zn(II) ions. We studied the stoichiometry, stability, and binding sites of Cu(II)/Ni(II)/Zn(II) complexes of two model peptides: XEN = Ac-DKPEEEEDGHGHAH (M. xenopi) and ABS = Ac-DKPAEEADHGHGHHGHAH (M. abscessus) in the pH range 2-11. In the case of Cu(II), Ni(II), and Zn(II) complexes of XEN and ABS, ABS always formed more stable complexes. For XEN, there seemed to be no preference for Ni(II) or Zn(II) ions. In contrast, for ABS, Zn(II) formed a complex that was slightly more stable than the one formed by Ni(II). This may be due to the 6 His residues, which preferentially interact with Zn(II) rather than Ni(II). The study identified that an equilibrium of complexes-known as polymorphism-may occur in ABS complexes. Therefore, distinct sets of histidine residues may be involved in metal binding.

Bacterial M10 metallopeptidase as a medicinal target - coordination chemistry of possible metal-based inhibition

Streptococcus pneumoniae is the most frequent cause of fatal bacterial pneumonia infection worldwide. Due to the spreading of antibiotic-resistant pathogens, it is important to search for new therapeutic and prevention strategies against bacterial infections. It is believed that the search for effective inhibitors of bacterial and pathogenic metallopeptidases could be one of the innovative strategies for the design of new antibiotics. Most of them contain zinc in the metal-binding site of the protein, which is a critical component for the biological activity of the enzyme. The main goal of this work is to determine the specificity of the interactions between the binding domain of the metallopeptidase from S. pneumoniae, and Zn(II). Considering the observed inhibitory role of copper towards the metallopeptidases, the next step is to analyze the formation of complexes with Cu(II) and Ni(II). The thermodynamic properties of Zn(II), Cu(II), and Ni(II) complexes were examined by potentiometry, NMR, MS, UV-Vis, CD, and EPR. The results show a similar coordination pattern, HExxHxxxxxH, for all three studied metals below pH 7. Moreover, the primary binding sites were established as the N-terminus in all cases. However, at a pH value of 7.4, the coordination and geometry of the formed complexes differ. The comparison of the stability of the formed complexes reveals that both Cu(II) and Ni(II) are able to displace Zn(II) from its binding site in the whole studied pH range. It opens a discussion on the catalytic zinc ion displacement possibilities by other divalent metal ions and the importance of this process in enzymatic inhibition.

Coordination Properties of the Zinc Domains of BigR4 and SmtB Proteins in Nickel Systems─Designation of Key Donors

The increasing number of antibiotic-resistant pathogens has become one of the foremost health problems of modern times. One of the most lethal and multidrug-resistant bacteria is Mycobacterium tuberculosis (Mtb), which causes tuberculosis (TB). TB continues to engulf health systems due to the significant development of bacterial multidrug-resistant strains. Mammalian immune system response to mycobacterial infection includes, but is not limited to, increasing the concentration of zinc(II) and other divalent metal ions in phagosome vesicles up to toxic levels. Metal ions are necessary for the survival and virulence of bacteria but can be highly toxic to organisms if their concentrations are not strictly controlled. Therefore, understanding the mechanisms of how bacteria use metal ions to maintain their optimum concentrations and survive under lethal environmental conditions is essential. The mycobacterial SmtB protein, one of the metal-dependent transcription regulators of the ArsR/SmtB family, dissociates from DNA in the presence of high concentrations of metals, activating the expression of metal efflux proteins. In this work, we explore the properties of α5 metal-binding domains of SmtB/BigR4 proteins (the latter being the SmtB homolog from nonpathogenic Mycobacterium smegmatis), and two mutants of BigR4 as ligands for nickel(II) ions. The study focuses on the specificity of metal–ligand interactions and describes the effect of mutations on the coordination properties of the studied systems. The results of this research reveal that the Ni(II)-BigR4 α5 species are more stable than the Ni(II)-SmtB α5 complexes. His mutations, exchanging one of the histidines for alanine, cause a decrease in the stability of Ni(II) complexes. Surprisingly, the lack of His102 resulted also in increased involvement of acidic amino acids in the coordination. The results of this study may help to understand the role of critical mycobacterial virulence factor—SmtB in metal homeostasis. Although SmtB prefers Zn(II) binding, it may also bind metal ions that prefer other coordination modes, for example, Ni(II). We characterized the properties of such complexes in order to understand the nature of mycobacterial SmtB when acting as a ligand for metal ions, given that nickel and zinc ArsR family proteins possess analogous metal-binding motifs. This may provide an introduction to the design of a new antimicrobial strategy against the pathogenic bacterium M. tuberculosis.

The histidine-rich α5 domains of SmtB (L4, Mycobacterium tuberculosis) and BigR4 (L1, Mycobacterium smegmatis) were studied as ligands for Ni(II). Point mutation analysis of L1 revealed that His102 and 106 preferably bind metal ions. The general Ni(II)-binding motif for both of the ligands was established as HX3HX3DX3HX2ED. L1 forms more stable complexes than L4 due to the stabilizing effect of arginine residues.

Nickel Carcinogenesis Mechanism: DNA Damage

Nickel (Ni) is known to be a major carcinogenic heavy metal. Occupational and environmental exposure to Ni has been implicated in human lung and nasal cancers. Currently, the molecular mechanisms of Ni carcinogenicity remain unclear, but studies have shown that Ni-caused DNA damage is an important carcinogenic mechanism. Therefore, we conducted a literature search of DNA damage associated with Ni exposure and summarized known Ni-caused DNA damage effects. In vitro and vivo studies demonstrated that Ni can induce DNA damage through direct DNA binding and reactive oxygen species (ROS) stimulation. Ni can also repress the DNA damage repair systems, including direct reversal, nucleotide repair (NER), base excision repair (BER), mismatch repair (MMR), homologous-recombination repair (HR), and nonhomologous end-joining (NHEJ) repair pathways. The repression of DNA repair is through direct enzyme inhibition and the downregulation of DNA repair molecule expression. Up to now, the exact mechanisms of DNA damage caused by Ni and Ni compounds remain unclear. Revealing the mechanisms of DNA damage from Ni exposure may contribute to the development of preventive strategies in Ni carcinogenicity.

Elucidating the mechanisms of nickel compound uptake: a review of particulate and nano-nickel endocytosis and toxicity

Nickel (Ni) is a worldwide pollutant and contaminant that humans are exposed to through various avenues resulting in multiple toxic responses - most alarming is its clear carcinogenic nature. A variety of particulate Ni compounds persist in the environment and can be distinguished by characteristics such as solubility, structure, and surface charge. These characteristics influence cellular uptake and toxicity. Some particulate forms of Ni are carcinogenic and are directly and rapidly endocytized by cells. A series of studies conducted in the 1980s observed this process, and we have reanalyzed the results of these studies to help elucidate the molecular mechanism of particulate Ni uptake. Originally the process of uptake observed was described as phagocytosis, however in the context of recent research we hypothesize that the process is macropinocytosis and/or clathrin mediated endocytosis. Primary considerations in determining the route of uptake here include calcium dependence, particle size, and inhibition through temperature and pharmacological approaches. Particle characteristics that influenced uptake include size, charge, surface characteristics, and structure. This discussion is relevant in the context of nanoparticle studies and the emerging interest in nano-nickel (nano-Ni), where toxicity assessments require a clear understanding of the parameters of particulate uptake and where establishment of such parameters is often obscured through inconsistencies across experimental systems. In this regard, this review aims to carefully document one system (particulate nickel compound uptake) and characterize its properties.

Epigenetics in metal carcinogenesis: nickel, arsenic, chromium and cadmium

Although carcinogenic metals have been known to disrupt a wide range of cellular processes the precise mechanism by which these exert their carcinogenic effects is not known. Over the last decade or two, studies in the field of metal carcinogenesis suggest that epigenetic mechanisms may play a role in metal-induced carcinogenesis. In this review we summarize the evidence demonstrating that exposure to carcinogenic metals such as nickel, arsenic, chromium, and cadmium can perturb DNA methylation levels as well as global and gene specific histone tail posttranslational modification marks. We also wish to emphasize the importance in understanding that gene expression can be regulated by both genetic and epigenetic mechanisms and both these must be considered when studying the mechanism underlying the toxicity and cell-transforming ability of carcinogenic metals and other toxicants, and aberrant changes in gene expression that occur during disease states such as cancer.

A zinc-finger like metal binding site in the nucleosome

UV spectroscopy demonstrated that chicken mononucleosomes bind Co(II) and Zn(II) ions at submicromolar concentrations in a tetrahedral mode, at a conserved zinc finger-like site, composed of Cys110 and His113 residues of both H3 molecules. Neither of these metal ions substituted for another, indicating a limited binding reversibility. Molecular modeling indicated that the tetrahedral site is formed by unhindered rotations around Calpha-Cbeta bonds in the side chains of the zinc binding residues. The resulting local rearrangement of the protein structure shields the bound metal ion from the solvent, explaining the observed lack of reversibility of the binding. Consequences of these findings for zinc homeostasis, metal toxicology and nucleosomal regulation are discussed.

Metal ion selectivity of oligopeptides

Metal binding affinity and selectivity of peptides are reviewed with a special emphasis on the high structural variety of peptide complexes. The most common structural type of these complexes is built up by the deprotonation and metal ion coordination of subsequent amide groups in the form of fused five-membered chelate rings. The metal ion selectivity of this process and the role of various anchoring groups are discussed in detail. The highest metal binding affinity of peptides is connected to the presence of two anchoring groups in appropriate location (the "double anchor"): e.g. the NH2-Xaa-Xaa-His/Cys/Asp/Met-Xaa sequence. Among the side chain donor functions, the imidazole of histidyl and thiolate of cysteinyl residues are the most effective ligating groups and their involvement in metal binding results in a great variety of different macrochelate or loop structures and/or formation of various polynuclear complexes. Examples of these structural motifs and their possible applications have been thoroughly discussed.

Two closely related nickel complexes have different effects on DNA damage and cell viability

Nickel is considered a weak carcinogen. It is known to interact with DNA and DNA-binding proteins. The ability of certain nickel compounds to cleave DNA has been exploited mainly for research purposes and less for developing new anticancer drugs. Here we compare the interactions of two closely related nickel complexes, [NiCR]2+ and [Ni(CR-2H)]2+, with DNA. CR stands for 2,12-dimethyl-3,7,11,17-tetraazabicyclo-[11.3.1]-heptadeca-1(17),2,11,13,15-pentaene. [NiCR]2+ has been used in the past as a structure-specific probe for RNA and DNA oligonucleotides in the presence of oxidizing agent but little is known about the biological effects of either complex. Our results show that [Ni(CR-2H)]2+ can damage DNA in vivo and in vitro in the absence of an added oxidizing agent and has an IC50 of 70 microM in human breast cancer cells whereas [NiCR]2+ and NiCl2 do not exhibit significant cytotoxicity. However, both [NiCR]2+ and [Ni(CR-2H)]2+ bind to the minor groove of double-stranded DNA.

Conference overview: Molecular mechanisms of metal toxicity and carcinogenesis

Chronic exposure to many heavy metals and metal-derivatives is associated with an increased risk of cancer, although the mechanisms of tumorigenesis are largely unknown. Approximately 125 scientists attended the 3rd Conference on Molecular Mechanisms of Metal Toxicity and Carcinogenesis and presented the latest research concerning these mechanisms. Major areas of focus included exposure assessment and biomarker identification, roles of ROS and antioxidants in carcinogenesis, mechanisms of metal-induced DNA damage, metal signalling, and the development of animal models for use in metal toxicology studies. Here we highlight some of the research presented, and summarize the conference proceedings.

Coordination mode and oxidation susceptibility of nickel(II) complexes with 2'-deoxyguanosine 5'-monophosphate and l-histidine

The formation of binary and ternary complexes of Ni(II) with two biologically relevant molecules, 2'-deoxyguanosine 5'-monophosphate (dGMP) and l-histidine (histidine or His) was characterized by potentiometry and UV-visible spectroscopy. For dGMP, the mononuclear complexes with stoichiometries NiH(2)L(+), NiHL and NiL(-) were found. In the mixed system the ternary complexes NiH(2)LA, NiHLA(-) and NiLA(2-) were detected. In binary systems, the Ni(II) ion coordinates to dGMP through the N-7 atom of its purine ring and indirectly through a water molecule bonded to the phosphate group, while in ternary complexes Ni(II) is bonded to all three histidine donors and directly to the phosphate group of dGMP. Both binary and ternary complexes are susceptible to oxidation by H(2)O(2), with the increased formation of 8-oxo-dGMP in the ternary system. The toxicological relevance of these findings stems from possible disturbance by the major biological Ni(II)-His complex of the nucleotide pools homeostasis through the formation of ternary species and oxidation promotion, as well as from 8-oxo-dGMP capacity to inhibit enzymatic elimination of promutagenic oxidized nucleotides from such pools.

Determination of the stability constants and oxidation susceptibility of nickel(II) complexes with 2'-deoxyguanosine 5'-triphosphate and L-histidine

The formation of binary Ni(II) complexes with 2'-deoxyguanosine 5'-triphosphate (dGTP, L) as well as ternary complexes thereof with L-histidine (His, A) was studied with the use of potentiometry and electronic absorption spectroscopy. In the binary and ternary systems, the complexes with stoichiometries NiH2L-, NiHL2-, NiL3- and NiH2LA2-, NiHLA3-, NiLA4- respectively, were detected. The ternary complexes are very stable at pH 7.4 and thus may constitute biologically relevant Ni(II) carriers in the cell. In the presence of hydrogen peroxide, the binary and ternary systems both generate hydroxyl radical-like species and undergo dGTP degradation with the formation of the 8-oxo-dGTP intermediate. The latter, along with dGTP complexation and degradation, may lead to mutagenesis and carcinogenesis due to base-mispairing properties of 8-oxoguanine and the disturbance in the physiological balance among the four canonical triphosphodeoxynucleotide substrates for DNA synthesis.

Correlations between complexation modes and redox activities of Ni(II)-GSH complexes

The formation of Ni(II) complexes of GSH in conditions of 4-fold GSH excess over Ni(II) was studied by potentiometric titrations, UV-vis and CD spectroscopies, and magnetic susceptibility measurements. The following set of complexes was obtained in the pH range of 6-12: NiHL, Ni(2)L(2)(2)(-), NiHL(2)(3)(-), NiL(2)(4)(-), and NiH(-)(1)L(2)(5)(-). The first of these is an octahedral species, coordinated through the donors of the Glu moiety of GSH, while the remaining ones are largely square-planar, with participation of the thiol in Ni(II) coordination. Magnetic moments indicate the presence of a spin equilibrium for Ni(2)L(2)(2)(-), NiHL(2)(3)(-), and NiL(2)(4)(-) complexes. Phosphate ions apparently decompose the Ni(2)L(2)(2)(-) complex, converting it into a monomeric, high spin, ternary species. Among the molecular forms of GSH, HL(2)(-) is the one most susceptible to air oxidation, due to a presence of ionic interactions between its protonated amine and deprotonated thiol moieties. The complexation of Ni(II) accelerates air oxidation of GSH in alkaline solutions by a factor of 4, but this effect is absent at neutral pH. The damage to plasmid DNA by H(2)O(2) is facilitated by Ni(II) ions and inhibited by excess of GSH. However, the analysis of the concentration profile of this process indicates that octahedral Ni(II) complexes with GSH are involved in the formation of double strand breaks. Finally, numerical simulations of intracellular Ni(II) distribution, made possible by the determination of stability constants of Ni(II) complexes of GSH, indicate that histidine and ATP, rather than GSH, may act as ligands for Ni(II) in vivo. Altogether, our results suggest that the direct impact of GSH on Ni(II) toxicity may be of a limited character.

Epigenetics and the environment

DNA methylation and histone modification promote changes in chromatin structure that may affect gene expression in a heritable manner without directly altering the genome. As such, these phenomena are considered to be epigenetic in nature and are believed to contribute to the normal processes of human development but also to aberrant disease states such as cancer. Epigenetic processes probably contribute mechanistically to toxicant-induced changes in gene expression and cancer. Nickel is a potent human carcinogen that has been shown to alter DNA methylation patterns and affect histone acetylation status. Both of these changes are associated with the proximity of the affected regions to heterochromatin. The two processes probably occur in concert in mammalian cells. However, in yeast cells, DNA methylation is absent, and nickel is capable of regulating gene expression through changes in acetylation of the lysine residues in the N terminal tail of histone H4. Arsenic is another important environmental carcinogen, and it is methylated during its metabolism. Hence, it has been proposed that arsenic metabolism may deplete intracellular methyl group stores and thereby lead to changes in DNA methylation that may be involved in carcinogenesis. However, the data concerning DNA methylation changes following arsenic exposure are equivocal, leading researchers to propose that DNA hypo- and hypermethylation are both important in the development of arsenic-induced cancers. Heightened awareness by toxicologists of the importance of epigenetics in normal human development and in carcinogenesis should lead to the identification of other toxicants that manifest their effects, at least in part, via epigenetic mechanisms.

Metal resistance in yeast mediated by the expression of a maize 20S proteasome alpha subunit

Transformation of yeast cells with a maize cDNA ZmPAA, encoding a 20S proteasome alpha-subunit, conferred resistance to nickel, cadmium and cobalt. This resistance is not linked to a modification of the intracellular nickel content, as no accumulation of nickel was measured between yeast cells transformed with a void vector or the ZmPAA cDNA. The abundance of the ZmPAA mRNA was increased in the shoots of maize plants upon nickel treatment. These results suggest that the proteasome might be involved in nickel resistance by scavenging metal oxidized proteins both in plants and yeast.

Induction of oxidative DNA damage by carcinogenic metals

The metal ions carcinogenic to humans are As, Be, Cd, Cr and Ni, and the candidates also include Co, Cu, Fe and Pt. A range of molecular mechanisms was proposed for these metals, reflecting their diverse chemical properties. The oxidative concept in metal carcinogenesis proposes that some complexes of the above metals (Co, Cr, Cu, Fe, Ni) formed in vivo undergo redox cycling, yielding reactive oxygen species and/or high valence metal ions which oxidize DNA. Some of the products of oxidative DNA damage, including 8-oxoguanine and strand breaks, induce mutations, which may lead to neoplastic transformation. The establishment of metal-binding modes in the cell nucleus and of their reactivity is crucial for the understanding of molecular events in metal carcinogenesis. We have proposed the binding sites for Ni(II) and Cu(II) in core histones (H3, H2A) and sperm protamines (HP2) and, using molecular models, provided evidence for the generation of promutagenic oxidative DNA damage by the bound metals.

Nickel resistance and chromatin condensation in Saccharomyces cerevisiae expressing a maize high mobility group I/Y protein

Expression of a maize cDNA encoding a high mobility group (HMG) I/Y protein enables growth of transformed yeast on a medium containing toxic nickel concentrations. No difference in the nickel content was measured between yeast cells expressing either the empty vector or the ZmHMG I/Y2 cDNA. The ZmHMG I/Y2 protein contains four AT hook motifs known to be involved in binding to the minor groove of AT-rich DNA regions. HMG I/Y proteins may act as architectural elements modifying chromatin structure. Indeed, a ZmHMG I/Y2-green fluorescent protein fusion protein was observed in yeast nuclei. Nickel toxicity has been suggested to occur through an epigenetic mechanism related to chromatin condensation and DNA methylation, leading to the silencing of neighboring genes. Therefore, the ZmHMG I/Y2 protein could prevent nickel toxicity by interfering with chromatin structure. Yeast cell growth in the presence of nickel and yeast cells expressing the ZmHMG I/Y2 cDNA increased telomeric URA3 gene silencing. Furthermore, ZmHMG I/Y2 restored a wild-type level of nickel sensitivity to the yeast (Delta)rpd3 mutant. Therefore, nickel resistance of yeast cells expressing the ZmHMG I/Y2 cDNA is likely achieved by chromatin structure modification, restricting nickel accessibility to DNA.

Extra-helical guanine interactions in DNA

We review the extra-helical guanine interactions present in many oligonucleotide crystals. Very often terminal guanines interact with other guanines in the minor groove of neighboring oligonucleotides through N2 x N3 hydrogen bonds. In other cases the interaction occurs with the help of Ni2+ ions. Guanine/netropsin stacking in the minor groove has also been found. From these studies we conclude that guanine may have multiple extra-helical interactions. In particular it may be considered a very effective minor groove binder, which could be used in the design of sequence selective binding drugs. Interactions through the major groove are seldom encountered, but might be present when DNA is stretched. Such interactions are also analyzed, since they might be important for homologous chromosome pairing during meiosis.

Molecular models in nickel carcinogenesis

Nickel compounds are known human carcinogens, but the exact molecular mechanisms of nickel carcinogenesis are not known. Due to their abundance, histones are likely targets for Ni(II) ions among nuclear macromolecules. This paper reviews our recent studies of peptide and protein models of Ni(II) binding to histones. The results allowed us to propose several mechanisms of Ni(II)-inflicted damage, including nucleobase oxidation and sequence-specific histone hydrolysis. Quantitative estimations of Ni(II) speciation, based on these studies, support the likelihood of Ni(II) binding to histones in vivo, and the protective role of high levels of glutathione. These calculations indicate the importance of histidine in the intracellular Ni(II) speciation.

Stacking interaction of guanine with netropsin in the minor groove of d(CGTATATACG)2

We present the structure of the decanucleotide d(CGTATATACG) determined by single crystal X-ray diffraction at 1.58 A resolution. A netropsin drug is found in the minor groove with guanine stacked on a pyrrole ring of the drug, a feature described here for the first time. The stacked guanine is an extra-helical base coming from the end of a neighbour oligonucleotide. This observation may open the way to the development of minor groove binding drugs with a higher sequence selectivity. The oligonucleotide is in the B-conformation, but the terminal base-pairs are disrupted: the cytosine residues are disordered while the guanine residues penetrate into the minor groove of neighbouring duplexes. Four hydrated Ni ions with octahedral co-ordination are found associated with the N7 atoms of each guanine. The high affinity of these ions with guanine suggests that they may be used as probes for specific guanine residues.